5Z1A

The crystal structure of Bacteroides fragilis beta-glucuronidase in complex with uronic isofagomine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Dissection of the substrate preference and structure of gut microbial-glucuronidases identifies the major bacteria causing xenobiotic toxicity

Dashnyam, P.Mudududdla, R.Hsieh, T.J.Lin, T.C.Lin, H.Y.Chen, P.Y.Hsu, C.Y.Lin, C.H.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative beta-galactosidase680Bacteroides fragilis NCTC 9343Mutation(s): 0 
Gene Names: BF9343_0320
EC: 3.2.1.31
UniProt
Find proteins for Q5LIC7 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2))
Explore Q5LIC7 
Go to UniProtKB:  Q5LIC7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5LIC7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SJ5 (Subject of Investigation/LOI)
Query on SJ5

Download Ideal Coordinates CCD File 
B [auth A](3S,4R,5R)-4,5-dihydroxypiperidine-3-carboxylic acid
C6 H11 N O4
SSMLJUWXZFXWSF-VPENINKCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.253α = 90
b = 103.135β = 90
c = 199.147γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references